Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/parser/interface.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 import os
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2 from abc import (
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3 ABCMeta,
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4 abstractmethod
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5 )
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6
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7 import six
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8
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9 from .util import _parse_name
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10
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11 NOT_IMPLEMENTED_MESSAGE = "Galaxy tool format does not yet support this tool feature."
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12
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13
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14 @six.python_2_unicode_compatible
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15 @six.add_metaclass(ABCMeta)
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16 class ToolSource(object):
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17 """ This interface represents an abstract source to parse tool
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18 information from.
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19 """
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20 default_is_multi_byte = False
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21
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22 @abstractmethod
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23 def parse_id(self):
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24 """ Parse an ID describing the abstract tool. This is not the
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25 GUID tracked by the tool shed but the simple id (there may be
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26 multiple tools loaded in Galaxy with this same simple id).
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27 """
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28
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29 @abstractmethod
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30 def parse_version(self):
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31 """ Parse a version describing the abstract tool.
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32 """
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33
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34 def parse_tool_module(self):
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35 """ Load Tool class from a custom module. (Optional).
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36
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37 If not None, return pair containing module and class (as strings).
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38 """
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39 return None
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40
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41 def parse_action_module(self):
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42 """ Load Tool class from a custom module. (Optional).
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43
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44 If not None, return pair containing module and class (as strings).
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45 """
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46 return None
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47
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48 def parse_tool_type(self):
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49 """ Load simple tool type string (e.g. 'data_source', 'default').
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50 """
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51 return None
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52
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53 @abstractmethod
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54 def parse_name(self):
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55 """ Parse a short name for tool (required). """
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56
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57 @abstractmethod
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58 def parse_description(self):
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59 """ Parse a description for tool. Longer than name, shorted than help. """
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60
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61 def parse_is_multi_byte(self):
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62 """ Parse is_multi_byte from tool - TODO: figure out what this is and
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63 document.
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64 """
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65 return self.default_is_multi_byte
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66
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67 def parse_display_interface(self, default):
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68 """ Parse display_interface - fallback to default for the tool type
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69 (supplied as default parameter) if not specified.
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70 """
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71 return default
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72
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73 def parse_require_login(self, default):
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74 """ Parse whether the tool requires login (as a bool).
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75 """
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76 return default
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77
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78 def parse_request_param_translation_elem(self):
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79 """ Return an XML element describing require parameter translation.
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80
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81 If we wish to support this feature for non-XML based tools this should
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82 be converted to return some sort of object interface instead of a RAW
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83 XML element.
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84 """
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85 return None
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86
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87 @abstractmethod
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88 def parse_command(self):
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89 """ Return string contianing command to run.
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90 """
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91
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92 def parse_expression(self):
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93 """ Return string contianing command to run.
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94 """
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95 return None
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96
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97 @abstractmethod
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98 def parse_environment_variables(self):
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99 """ Return environment variable templates to expose.
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100 """
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101
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102 def parse_home_target(self):
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103 """Should be "job_home", "shared_home", "job_tmp", "pwd", or None.
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104 """
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105 return "pwd"
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106
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107 def parse_tmp_target(self):
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108 """Should be "pwd", "shared_home", "job_tmp", "job_tmp_if_explicit", or None.
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109 """
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110 return "job_tmp"
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111
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112 def parse_tmp_directory_vars(self):
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113 """Directories to override if a tmp_target is not None."""
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114 return ["TMPDIR", "TMP", "TEMP"]
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115
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116 def parse_docker_env_pass_through(self):
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117 return ["GALAXY_SLOTS", "HOME", "_GALAXY_JOB_HOME_DIR", "_GALAXY_JOB_TMP_DIR"] + self.parse_tmp_directory_vars()
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118
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119 @abstractmethod
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120 def parse_interpreter(self):
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121 """ Return string containing the interpreter to prepend to the command
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122 (for instance this might be 'python' to run a Python wrapper located
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123 adjacent to the tool).
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124 """
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125
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126 @abstractmethod
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127 def parse_interactivetool(self):
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128 """ Return InteractiveTool entry point templates to expose.
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129 """
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130
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131 def parse_redirect_url_params_elem(self):
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132 """ Return an XML element describing redirect_url_params.
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133
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134 If we wish to support this feature for non-XML based tools this should
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135 be converted to return some sort of object interface instead of a RAW
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136 XML element.
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137 """
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138 return None
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139
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140 def parse_version_command(self):
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141 """ Parse command used to determine version of primary application
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142 driving the tool. Return None to not generate or record such a command.
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143 """
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144 return None
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145
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146 def parse_version_command_interpreter(self):
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147 """ Parse command used to determine version of primary application
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148 driving the tool. Return None to not generate or record such a command.
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149 """
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150 return None
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151
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152 def parse_parallelism(self):
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153 """ Return a galaxy.jobs.ParallismInfo object describing task splitting
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154 or None.
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155 """
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156 return None
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157
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158 def parse_hidden(self):
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159 """ Return boolean indicating whether tool should be hidden in the tool menu.
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160 """
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161 return False
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162
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163 def parse_sanitize(self):
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164 """ Return boolean indicating whether tool should be sanitized or not.
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165 """
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166 return True
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167
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168 def parse_refresh(self):
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169 """ Return boolean indicating ... I have no clue...
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170 """
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171 return False
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172
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173 @abstractmethod
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174 def parse_requirements_and_containers(self):
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175 """ Return pair of ToolRequirement and ContainerDescription lists. """
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176
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177 @abstractmethod
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178 def parse_input_pages(self):
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179 """ Return a PagesSource representing inputs by page for tool. """
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180
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181 def parse_provided_metadata_style(self):
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182 """Return style of tool provided metadata file (e.g. galaxy.json).
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183
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184 A value of of "default" indicates the newer galaxy.json style
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185 (the default for XML-based tools with profile >= 17.09) and a value
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186 of "legacy" indicates the older galaxy.json style.
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187
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188 A short description of these two styles can be found at
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189 https://github.com/galaxyproject/galaxy/pull/4437.
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190 """
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191 return "default"
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192
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193 def parse_provided_metadata_file(self):
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194 """Return location of provided metadata file (e.g. galaxy.json)."""
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195 return "galaxy.json"
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196
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197 @abstractmethod
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198 def parse_outputs(self, tool):
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199 """ Return a pair of output and output collections ordered
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200 dictionaries for use by Tool.
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201 """
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202
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203 @abstractmethod
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204 def parse_strict_shell(self):
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205 """ Return True if tool commands should be executed with
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206 set -e.
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207 """
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208
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209 @abstractmethod
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210 def parse_stdio(self):
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211 """ Builds lists of ToolStdioExitCode and ToolStdioRegex objects
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212 to describe tool execution error conditions.
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213 """
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214 return [], []
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215
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216 @abstractmethod
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217 def parse_help(self):
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218 """ Return RST definition of help text for tool or None if the tool
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219 doesn't define help text.
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220 """
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221
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222 @abstractmethod
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223 def parse_profile(self):
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224 """ Return tool profile version as Galaxy major e.g. 16.01 or 16.04.
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225 """
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226
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227 @abstractmethod
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228 def parse_python_template_version(self):
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229 """
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230 Return minimum python version that the tool template has been developed against.
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231 """
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232
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233 @property
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234 def macro_paths(self):
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235 return []
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236
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237 @property
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238 def source_path(self):
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239 return None
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240
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241 def paths_and_modtimes(self):
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242 paths_and_modtimes = {p: os.path.getmtime(p) for p in self.macro_paths}
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243 if self.source_path:
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244 paths_and_modtimes[self.source_path] = os.path.getmtime(self.source_path)
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245 return paths_and_modtimes
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246
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247 def parse_tests_to_dict(self):
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248 return {'tests': []}
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249
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250 def __str__(self):
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251 source_path = self.source_path
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252 if source_path:
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253 as_str = u'%s[%s]' % (self.__class__.__name__, source_path)
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254 else:
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255 as_str = u'%s[In-memory]' % (self.__class__.__name__)
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256 return as_str
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257
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258
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259 class PagesSource(object):
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260 """ Contains a list of Pages - each a list of InputSources -
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261 each item in the outer list representing a page of inputs.
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262 Pages are deprecated so ideally this outer list will always
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263 be exactly a singleton.
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264 """
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265
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266 def __init__(self, page_sources):
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267 self.page_sources = page_sources
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268
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269 @property
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270 def inputs_defined(self):
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271 return True
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272
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273
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274 @six.add_metaclass(ABCMeta)
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275 class PageSource(object):
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276
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277 def parse_display(self):
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278 return None
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279
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280 @abstractmethod
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281 def parse_input_sources(self):
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282 """ Return a list of InputSource objects. """
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283
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284
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285 @six.add_metaclass(ABCMeta)
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286 class InputSource(object):
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287 default_optional = False
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288
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289 def elem(self):
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290 # For things in transition that still depend on XML - provide a way
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291 # to grab it and just throw an error if feature is attempted to be
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292 # used with other tool sources.
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293 raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
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294
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295 @abstractmethod
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296 def get(self, key, value=None):
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297 """ Return simple named properties as string for this input source.
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298 keys to be supported depend on the parameter type.
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299 """
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300
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301 @abstractmethod
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302 def get_bool(self, key, default):
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303 """ Return simple named properties as boolean for this input source.
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304 keys to be supported depend on the parameter type.
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305 """
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306
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307 def parse_label(self):
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308 return self.get("label")
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309
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310 def parse_name(self):
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311 """Return name of an input source
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312 returns the name or if absent the argument property
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313 In the latter case, leading dashes are stripped and
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314 all remaining dashes are replaced by underscores.
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315 """
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316 return _parse_name(self.get('name'), self.get('argument'))
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317
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318 def parse_help(self):
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319 return self.get("help")
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320
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321 def parse_sanitizer_elem(self):
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322 """ Return an XML description of sanitizers. This is a stop gap
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323 until we can rework galaxy.tools.parameters.sanitize to not
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324 explicitly depend on XML.
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325 """
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326 return None
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327
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328 def parse_validator_elems(self):
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329 """ Return an XML description of sanitizers. This is a stop gap
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330 until we can rework galaxy.tools.parameters.validation to not
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331 explicitly depend on XML.
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332 """
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333 return []
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334
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335 def parse_optional(self, default=None):
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336 """ Return boolean indicating wheter parameter is optional. """
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337 if default is None:
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338 default = self.default_optional
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339 return self.get_bool("optional", default)
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340
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341 def parse_dynamic_options_elem(self):
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342 """ Return an XML elemnt describing dynamic options.
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343 """
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344 return None
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345
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346 def parse_static_options(self):
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347 """ Return list of static options if this is a select type without
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348 defining a dynamic options.
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349 """
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350 return []
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351
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352 def parse_conversion_tuples(self):
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353 """ Return list of (name, extension) to describe explicit conversions.
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354 """
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355 return []
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356
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357 def parse_nested_inputs_source(self):
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358 # For repeats
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359 raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
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360
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361 def parse_test_input_source(self):
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362 # For conditionals
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363 raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
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364
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365 def parse_when_input_sources(self):
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366 raise NotImplementedError(NOT_IMPLEMENTED_MESSAGE)
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367
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368
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369 class TestCollectionDef(object):
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370
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371 def __init__(self, attrib, name, collection_type, elements):
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372 self.attrib = attrib
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373 self.collection_type = collection_type
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374 self.elements = elements
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375 self.name = name
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376
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377 @staticmethod
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378 def from_xml(elem, parse_param_elem):
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379 elements = []
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380 attrib = dict(elem.attrib)
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381 collection_type = attrib["type"]
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382 name = attrib.get("name", "Unnamed Collection")
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383 for element in elem.findall("element"):
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384 element_attrib = dict(element.attrib)
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385 element_identifier = element_attrib["name"]
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386 nested_collection_elem = element.find("collection")
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387 if nested_collection_elem is not None:
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388 element_definition = TestCollectionDef.from_xml(nested_collection_elem, parse_param_elem)
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389 else:
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390 element_definition = parse_param_elem(element)
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391 elements.append({"element_identifier": element_identifier, "element_definition": element_definition})
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392
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393 return TestCollectionDef(
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394 attrib=attrib,
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395 collection_type=collection_type,
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396 elements=elements,
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397 name=name,
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398 )
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399
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400 def to_dict(self):
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401 def element_to_dict(element_dict):
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402 element_identifier, element_def = element_dict["element_identifier"], element_dict["element_definition"]
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403 if isinstance(element_def, TestCollectionDef):
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404 element_def = element_def.to_dict()
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405 return {
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406 "element_identifier": element_identifier,
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407 "element_definition": element_def,
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408 }
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409
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410 return {
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411 "model_class": "TestCollectionDef",
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412 "attributes": self.attrib,
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413 "collection_type": self.collection_type,
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414 "elements": list(map(element_to_dict, self.elements or [])),
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415 "name": self.name,
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416 }
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417
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418 @staticmethod
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419 def from_dict(as_dict):
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420 assert as_dict["model_class"] == "TestCollectionDef"
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421
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422 def element_from_dict(element_dict):
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423 if "element_definition" not in element_dict:
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424 raise Exception("Invalid element_dict %s" % element_dict)
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425 element_def = element_dict["element_definition"]
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426 if element_def.get("model_class", None) == "TestCollectionDef":
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427 element_def = TestCollectionDef.from_dict(element_def)
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428 return {"element_identifier": element_dict["element_identifier"], "element_definition": element_def}
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429
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430 return TestCollectionDef(
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431 attrib=as_dict["attributes"],
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432 name=as_dict["name"],
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433 elements=list(map(element_from_dict, as_dict["elements"] or [])),
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434 collection_type=as_dict["collection_type"],
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435 )
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436
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437 def collect_inputs(self):
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438 inputs = []
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439 for element in self.elements:
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440 value = element["element_definition"]
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441 if isinstance(value, TestCollectionDef):
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442 inputs.extend(value.collect_inputs())
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443 else:
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444 inputs.append(value)
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445 return inputs
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446
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447
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448 class TestCollectionOutputDef(object):
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449
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450 def __init__(self, name, attrib, element_tests):
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451 self.name = name
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452 self.collection_type = attrib.get("type", None)
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453 count = attrib.get("count", None)
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454 self.count = int(count) if count is not None else None
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455 self.attrib = attrib
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456 self.element_tests = element_tests
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457
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458 @staticmethod
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459 def from_dict(as_dict):
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460 return TestCollectionOutputDef(
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461 name=as_dict["name"],
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462 attrib=as_dict["attributes"],
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463 element_tests=as_dict["element_tests"],
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464 )
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465
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466 def to_dict(self):
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467 return dict(
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468 name=self.name,
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469 attributes=self.attrib,
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470 element_tests=self.element_tests
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471 )